A variety of unconventional materials, including biological nanostructures, organic and hybrid semiconductors, as well as monolayer, and other low-dimensional systems, are actively explored. They are usually incompatible with standard lithographic techniques that use harsh organic solvents and other detrimental processing. Here, a new class of green and gentle lithographic resists, compatible with delicate materials and capable of both top-down and bottom-up fabrication routines is developed. To demonstrate the excellence of this approach, devices with sub-micron features are fabricated on organic semiconductor crystals and individual animal's brain microtubules. Such structures are created for the first time, thanks to the genuinely water-based lithography, which opens an avenue for the thorough research of unconventional delicate materials at the nanoscale.